Phylogeny and proposed circumscription of Breynia, Sauropus and Synostemon (Phyllanthaceae), based on chloroplast and nuclear DNA sequences

2012 ◽  
Vol 25 (5) ◽  
pp. 313 ◽  
Author(s):  
Kanchana Pruesapan ◽  
Ian R. H. Telford ◽  
Jeremy J. Bruhl ◽  
Peter C. van Welzen
Keyword(s):  
Bayesian Inference ◽  
Dna Sequences ◽  
Dna Markers ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Morphological Features ◽  
Monophyletic Group ◽  
Infrageneric Classification ◽  
Generic Rank ◽  
Phylogenetic Resolution

Previous estimates of phylogeny in the Phyllanthaceae, Phyllantheae, have been hampered by undersampling of species from morphologically distinctive groups and using too few gene regions. To increase the phylogenetic resolution, sequences of two nuclear (ITS1–5.8S–ITS2) and Phytochrome C (PHYC)) and two non-coding chloroplast (accD–psaI, trnS–trnG) DNA markers were analysed using maximum parsimony and Bayesian inference with expanded sampling in Breynia, Glochidion, Sauropus and Synostemon. Our results supported reinstatement of Synostemon, previously included in Sauropus s.str., to generic rank, and provided evidence towards its future infrageneric classification. The results also indicated expansion of Breynia to include Sauropus s.str.; this combined monophyletic group consists of two strongly supported clades. Finally, we showed monophyly for Glochidion, which is sister to Phyllanthus subg. Phyllanthodendron, both still remaining undersampled. Morphological features characteristic of Breynia, Sauropus and Synostemon are discussed, as well as the desirability of dividing Phyllanthus into smaller genera.

Description of a new genus and two new species of killifish (Cyprinodontiformes: Nothobranchiidae) from West Africa, with a discussion of the taxonomic status of Aphyosemion maeseni Poll, 1941

Zootaxa ◽  
2009 ◽  
Vol 2294 (1) ◽  
pp. 1-22 ◽  
Author(s):  
RAINER SONNENBERG ◽  
ECKHARD BUSCH
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
New Genus ◽  
Nuclear Dna ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Color Pattern ◽  
Monophyletic Group ◽  
Morphological Data ◽  
Adult Males

The phylogeny of the West African genus Archiaphyosemion was studied with mitochondrial and nuclear DNA sequences. The results of the combined dataset presented here did not support a monophyletic group. After the exclusion of the type species of the genus, A. guineense, the remaining species form a well-supported monophyletic group. Based on these molecular results and supported by morphological data, we suggest a new name for this group, Nimbapanchax, new genus. Additionally, based on a recent collection in Guinea, two new Nimbapanchax species were described. The taxon Nimbapanchax leucopterygius, new species, is described for a nothobranchiid fish formerly misidentified as Archiaphyosemion maeseni (Poll, 1941). Nimbapanchax melanopterygius, new species, is described from the Mount Nimba region in southeastern Guinea. Both new Nimbapanchax species are clearly distinguished from their congeners by the coloration pattern of adult males. The results of the DNA data support the assumption based on color pattern and morphological characters that the new described species are sister taxa. The type of Aphyosemion maeseni Poll, 1941 was reexamined and transferred to the genus Epiplatys, a decision based on diagnostic morphological characters.

scholarly journals Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability

Botany ◽  
2016 ◽  
Vol 94 (9) ◽  
pp. 863-884 ◽  
Author(s):  
David S. Gernandt ◽  
Garth Holman ◽  
Christopher Campbell ◽  
Matthew Parks ◽  
Sarah Mathews ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Consensus Methods ◽  
Topological Stability ◽  
Branch Support ◽  
Tree Topologies ◽  
Cone Scale

Relationships of living and fossil Pinaceae were inferred using parsimony and Bayesian inference of morphological characters and plastid and nuclear DNA sequences. When considering extant taxa only, adding molecular to morphological characters resulted in markedly increased resolution and branch support compared with analysis of morphology alone. Including 45 fossil taxa resulted in drastically decreased resolution in morphology-based consensus trees. We evaluated the effect on branch support and resolution of including DNA sequences, deleting fossils lacking information for cone scale apices and seeds, using reduced consensus methods, and using implied weighting, and found that the greatest improvements were found by including DNA sequences and using implied weighting. The tree topologies from parsimony and Bayesian inference confirm previous findings that the fossil genus Pseudoaraucaria and a few species of Pityostrobus from the Lower Cretaceous are related to abietoid genera, and that other species of Pityostrobus are pinoid and closely related to Pinus. Focusing phylogenetic analyses on the most complete fossil cones, specifically those that are anatomically preserved and include both cone scale apices and seeds, and taking into account homoplasy, resulted in the clearest hypotheses for the timing and sequence of diversification in the family.

Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA psbI–5′trnK(UUU) sequences, with emphasis on the North American Endemics clade

Botany ◽  
2008 ◽  
Vol 86 (9) ◽  
pp. 1039-1064 ◽  
Author(s):  
Stephen R. Downie ◽  
Deborah S. Katz-Downie ◽  
Feng-Jie Sun ◽  
Chang-Shook Lee
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Intergenic Spacers ◽  
Rdna Its ◽  
The North

Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.

scholarly journals Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences

2017 ◽  
Vol 8 ◽  
Author(s):  
Wenpan Dong ◽  
Chao Xu ◽  
Wenqing Li ◽  
Xiaoman Xie ◽  
Yizeng Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Chloroplast Genomes ◽  
Phylogenetic Resolution

scholarly journals Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex

Phytotaxa ◽  
2013 ◽  
Vol 91 (1) ◽  
pp. 1 ◽  
Author(s):  
MARCO MUCCIARELLI ◽  
MICHAEL F. FAY
Keyword(s):  
Dna Fingerprinting ◽  
Dna Sequences ◽  
Dna Markers ◽  
Nuclear Dna ◽  
Plastid Dna ◽  
Genetic Isolation ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Matk Gene ◽  
Length Variable

A phylogenetic analysis based on combined DNA sequences of the partial matK gene and the rpl16 intron showed that the rare alpine endemic Fritillaria tubiformis subsp. moggridgei (Liliaceae) and the more widespread F. tubiformis var. burnatii are exclusively related. A genetic study used plastid DNA markers, due to limits imposed by nuclear DNA fingerprinting in species with large genomes, to study variation within and between populations. Five length-variable homopolymer repeats (polyA and polyT) and four regions with one or two insertion/deletions (indels) of different lengths were identified. Of the total of 56 plastid haplotypes obtained, 32 were fixed in the seven populations of subsp. moggridgei and the rest were variable in var. burnatii. Analysis of molecular variance (AMOVA) showed higher genetic variation among rather than within subsp. moggridgei populations. Indel mutations, on the other hand, were fundamental in distinguishing the two taxa.

scholarly journals A large phylogeny of turtles (Testudines) using molecular data

2012 ◽  
Vol 81 (3) ◽  
pp. 147-158j ◽  
Author(s):  
Jean-Michel Guillon ◽  
Loreleï Guéry ◽  
Vincent Hulin ◽  
Marc Girondot
Keyword(s):  
Dna Sequences ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Body Plan ◽  
Monophyletic Group ◽  
Turtle Species ◽  
Species Phylogeny ◽  
Phylogenetic Resolution ◽  
Competing Hypotheses

Turtles (Testudines) form a monophyletic group with a highly distinctive body plan. The taxonomy and phylogeny of turtles are still under discussion, at least for some clades. Whereas in most previous studies, only a few species or genera were considered, we here use an extensive compilation of DNA sequences from nuclear and mitochondrial genes for more than two thirds of the total number of turtle species to infer a large phylogeny for this taxon. Our results enable us to discuss previous hypotheses on species phylogeny or taxonomy. We are thus able to discriminate between competing hypotheses and to suggest taxonomical modifications. Finally, we pinpoint the remaining ambiguities for this phylogeny and the species for which new sequences should be obtained to improve phylogenetic resolution.

scholarly journals Phylogenetic relationships of Discyphus scopulariae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences: evidence supporting recognition of a new subtribe, Discyphinae

Phytotaxa ◽  
2014 ◽  
Vol 173 (2) ◽  
pp. 127 ◽  
Author(s):  
GERARDO A. SALAZAR ◽  
Cássio Van den Berg ◽  
ALEX POPOVKIN
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Floral Morphology ◽  
Systematic Position ◽  
Morphological Differences ◽  
Early Radiation ◽  
Molecular Trees

The monospecific genus Discyphus, previously considered a member of Spiranthinae (Orchidoideae: Cranichideae), displays both vegetative and floral morphological peculiarities that are out of place in that subtribe. These include a single, sessile, cordate leaf that clasps the base of the inflorescence and lies flat on the substrate, petals that are long-decurrent on the column, labellum margins free from sides of the column and a column provided with two separate, cup-shaped stigmatic areas. Because of its morphological uniqueness, the phylogenetic relationships of Discyphus have been considered obscure. In this study, we analyse nucleotide sequences of plastid and nuclear DNA under maximum parsimony and maximum likelihood criteria with the aim of clarifying its systematic position and discussing its peculiar morphology in an explicit phylogenetic context. Our analyses failed to support inclusion of Discyphus in Spiranthinae, signifying instead that this genus represents an additional isolated lineage of “core spiranthids.” The notable morphological disparity among such major lineages, as compared with the short internal branches subtending them in the molecular trees, would support the hypothesis that Discyphus represents a relict from an early radiation that also gave rise to Cranichidinae and Spiranthinae, putatively driven by adaptation to different pollinators given the morphological differences in floral morphology among these taxa.

Molecular Phylogeny of Coprophanaeus (Megaphanaeus) d’Olsoufieff, 1924 (Coleoptera: Scarabaeidae: Scarabaeinae) and the position of C. bellicosus

2020 ◽  
Vol 51 (2) ◽  
pp. 241-255 ◽  
Author(s):  
Maria E. Maldaner ◽  
Fernando Z. Vaz-de-Mello ◽  
Daniela M. Takiya ◽  
Daniela C. Ferreira
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Maximum Parsimony ◽  
Phylogenetic Inference ◽  
Sister Group ◽  
Monophyletic Group ◽  
Valid Species ◽  
Nuclear Marker

Coprophanaeus (Megaphanaeus) d’Olsoufieff, 1924 has four valid species: C. lancifer (Linné, 1767), C. ensifer (Germar, 1821), C. bonariensis (Gory, 1844) and C. bellicosus (Olivier, 1789). However, authors disagree about the placement of C. bellicosus. Thus, our aims were (I) to test if Megaphanaeus is a monophyletic group and (II) verify to which subgenus C. bellicosus belongs. We sequenced three mitochondrial and one nuclear marker for ten Phanaeini species: COI (672bp), COI-II (1326bp), 16S (527bp) and 28S (994bp). For fifteen species we sequenced two markers, COI (681pb) and 16S (532pb). Both matrices were analyzed under three methods of phylogenetic inference: Maximum Parsimony, Maximum Likelihood, and Bayesian Inference. Megaphanaeus is here considered monophyletic including C. bellicosus as sister-group to (C. bonariensis (C. lancifer + C. ensifer)). All analyses recovered the non-monophyly of both C. lancifer and C. ensifer, because of a population of C. lancifer grouped with C. ensifer specimens.

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